title: GB1-1

city: Heidelberg

first: Haikun

address: INF 581

country: Germany

institute: DKFZ

data_processing:
RTA 1.18.64 was used for base-calling
For all single-cell/bulk libraries from neural stem cells or brain tumours, we obtained the gene expression profiles via mapping the sequencing reads to mouse mm10 transcriptome by RSEM (v1.3.0) (Li and Dewey, 2011). For single cells from brain tumours, we kept cells with 200 to 3500 genes and less than 10% of reads on mitochondrial genes and projected the cells into low dimension space using Monocle (Qiu et al., 2017; Trapnell et al., 2014) in R (R Core Team, 2018). We calculated the spearman correlation coefficient for single cells in neural stem cell populations and brain tumour populations using log2 transformed TPM value.
We used the R package DESeq2 (Love et al., 2014) to estimate the differentially expressed genes between bulk Tlx-GFP+/dsRed+ and Tlx-GFP-/dsRed+ using the estimated counts from RSEM results. The statistcally signficant genes were selected with fdr <= 0.1. Heatmaps for selected genes were produced with ComplexHeatmap (Gu et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: csv

source_name: mice brain tumors

growth_protocol: Mice were housed according to international standard conditions and all animal experiments complied with local and international guidelines for the use of experimental animals.

extract_protocol:
RNA extraction using the Arcturus PicoPure RNA Isolation kit was performed according to the manufacturer’s protocol (Life technologies). Briefly, 100 ul of extraction buffer was added to the cells, followed by brief incubation at room temperatue. While the lysate was incubated, the purification column was wetted (Pre-condition) by adding 250 ul of condition buffer, followed by centrifugation at 16,000 × g for 1 min. 100 ul of 70% ethanol was then added to the lysate, mixed well and the whole mixture was transferred to the prepared purification columns. Purification columns were centrifuged for 2 min at 100 × g, followed by centrifuging at 16,000 × g for 30 sec to remove flow through. 100 ul of wash buffer 1 was added to the purification columns, which were then centrifuged for 1 min at 8,000 × g. DNase treatment may was performed directly within the purification column. 10 µl DNase I stock solution (Qiagen, catalog#79254) was mixed with 30 µL Buffer RDD. 40 µL DNase incubation mix was applied directly into the purification column membrane followed by Incubation at room temperature for 15 minutes. 40 ul of wash buffer 1 was added to the purification columns, which were then centrifuged for 15 seconds at 8,000 × g. After that, 100 ul of wash buffer 2 was added to the purification columns, which were then centrifuged for 1 min at 8,000 × g. Another 100 ul of wash buffer 2 was added to the purification columns. Purification columns were centrifuged at 16,000 × g for 2 min. Another spin at 16,000 × g for 1 min was performed to remove the wash residue in the columns. Purification columns were transferred to new Eppendorf tubes and 11 ul of elution buffer was carefully added onto the column membrane followed by 1 min incubation at room temperature. Purification Columns were centrifuged at 1,000 × g for 1 min, and subsequently at 16,000 × g for 1 min to elute RNA. 10 ul of RNA solution was obtained.
Libraries were constructed using the Nextera XT kit as recommended by the manufacturer (Illumina, San Diego, USA). 0.5 ng of cDNA was tagmented, utilizing 5 μl of Amplicon Tagment Mix with 10 μl Tagment DNA Buffer. Tagmentation reaction was performed by incubation for 20 min at 55°C. Next, index primers were added together with Nextera PCR Master Mix. Tagmented cDNA was amplified by limited-cycle PCR (10 cycles). Libraries were purified using AMPure beads (Beckman Coulter, High Wycombe, UK) and quality validated using Agilent 2100 BioAnalyzer. Libraries were normalized and 8 nM pooled libraries were then sequenced on Illumina HiSeq2000.

treatment_protocol: FACS Sorting.Brain tumor tissues were isolated in Phosphate buffered saline solution (PBS) and enzymatically dissociated with 0.05% Trypsin/EDTA (Gibco) in HBSS containing 2mM glucose at 37°C for 30 min. During incubation, the tissue was repeatedly triturated with a fire polished Pasteur pipette. Enzyme activity was stopped by addition of equal volume of 4% BSA in Earle’s Balanced Salt Solution (EBSS, Gibco). The cell suspension was filtered through a 70μm cell strainer and centrifuged at 1200 rpm for 5 min and the pellet was re-suspended in 0.9 M sucrose in 0.5 x HBSS (Gibco). After further centrifugation for 20 min at 2000 rpm the cell pellet was re-suspended in 2 ml of 4 % BSA in EBSS solution and placed on top of 12 ml of 4 % BSA in EBSS solution, centrifuged again for 9 min at 1500 rpm.  The resulting pellet was then suspended in PBS containing Recombinant RNase Inhibitor, 1 unit/μl reaction (Clontech). After incubation with PI (1:1000) for 2 minutes; either the single cells or 1000 cells per tube were sorted at a FACS Aria (BD). Two population of cells were sorted, RFP positive and RFP / Tlx-GFP positive cells.

tag: mouse number

value: mouse one

tag: strain background

value: Tlx-GFP;Ntv-a mice

tag: genotype/variation

value: RCAS-AKT, RCAS-PDGFB and RCAS-RFP retroviruses transfection

tag: cell types

value: brain tumor stem cells

tag: sequencing type

value: bulk RNAseq


title: RB1-1

status: Public on May 01 2024

type: SRA

last: Liu

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

value: brain tumor cells


title: RB1-4


title: RB1-2


title: GB1-3


title: APP/PS1_12M_rep3

type: RNA

city: Nan Chong

first: Zhuoze

last: Wu

address: Dongshun Road, Gaoping District

country: China

institute: North Sichuan Medical College

description: gene expression in the hippocampus of 12months old APP/PS1 mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

source_name: hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The age-appropriate mice will be sacrificed and their bilateral hippocampus will be separated into a centrifuge tube respectively and frozen in liquid nitrogen.

tag: tissue

value: hippocampus

tag: genotype

tag: age


title: C57_3M_rep1

description: gene expression in the hippocampus of 3months old C57 mice


title: PRS5

city: Durham

first: Christopher

middle: L

last: Holley

state: NC

address: 2301 Erwin Rd

country: USA

institute: Duke University

data_processing:
Library strategy: RibOxi-seq
Paired end reads are first merged into single reads using bbmerge (v38.86) with a correction step (bbmerge-auto.sh ecco=t mix=t) before actual merging (bbmerge-auto.sh minoverlap=6 mininsert=20 mininsert0=20).
Partial 3' adapter is removed using cutadapt v2.10 (cutadapt --discard-untrimmed --minimum-length 20 -a CTGTAGGCACCATCAATGAC  -e 0.1 ), followed by moving the 5' random quadruplemer to read identifier line using move-umi.py from the riboxi-seq pipeline (move_umi.py -l 4 -i ATCACG -a ATCACGCTGTAGGCACCATCAATGAC -m 'pipeline'). Finally, cutadapt is used once again to remove reads that does not contain a fixed barcode at 3' end (cutadapt --discard-untrimmed --minimum-length 20 -a ATCACG -e 0.01 ).
Trypanosoma brucei brucei TREU927 small RNA transcript sequences were used to build STAR index (STAR version 2.7.5c). The Alignment was then done with STAR (STAR --outMultimapperOrder Random --outFilterMismatchNoverLmax 0.1 --alignEndsType EndToEnd --outSAMtype BAM SortedByCoordinate)
samtools is then used to index the resulting bam files before running umi_tools v1.01 to deduplicate aligned reads.
bedtools v2.29.2 was used with bamtobed option to generate bed files for each sample. The bedfiles were then loaded in R and all rows with "-" strands were removed. Reads 3' counts were calculated by summing up all rows that have the same "end" positions. Mean riboxi score for each position is then calculated by first calculating score per position for each sample (position/(average(position-1, position+1)+1)) followed by average each position across all samples.  Candidate sites are called using mean counts of 10 and score-mean of 4.
Supplementary_files_format_and_content: Raw 3' end counts
Supplementary_files_format_and_content: candidate sites with scores

organism: Trypanosoma brucei brucei TREU927

source_name: T. brucei cells

growth_protocol: Trypanosoma brucei parasites were grown in SDM-79 medium supplemented with 10% fetal calf serum at 27oC.

extract_protocol:
Whole cell extracts were prepared from 5x10^9 T. brucei cells in a buffer containing 24 mM KCl, 20 mM Tris-pH7.8 and 10 mM MgCl2. RNPs were extracted with 300 mM KCl, and the ribosomes were removed by centrifugation for 3 hr at 35,000 rpm in a Beckman 70.1Ti rotor (150000 x g). The supernatant containing the post-ribosomal supernatant (PRS) was deproteinized by digestion with proteinase K (Roche) (100 ug/ml in 1% SDS for 30 min at 37oC), and RNA was prepared using TRIzol (Sigma) reagent.
Libraries were created following the updated RibOxi-seq protocol (https://link.springer.com/protocol/10.1007%2F978-1-0716-1851-6_22). Fragmentation step was modified to use 250ng small RNA for benzonase digestion with fragmentation of 30 minutes instead of the much longer reaction time the original protocol calls for.

treatment_protocol: RNA was subjected to fragmentation using Benzonase and several steps of oxidation, β-elimination, and dephosphorylation, thus allowing the enrichment of Nm at 3'-end of fragmented RNAs.

tag: cell type

value: T. brucei cells

tag: developmental stage

value: Procyclic

tag: fraction

value: small RNAs


title: DMSO_P1_G05_S173, Smart-seq2 (multi-omics)

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

description: Smartseq2_mouse_multiomics_processed_TPM.tsv

data_processing:
We processed Smart-seq2 data from raw reads to gene expression matrices as previously described in Neftel et al, 2019. We used bcl2fastq to generate demultiplexed FASTQ files, and aligned the resulting paired-end scRNA-seq reads to the reference transcriptome using Bowtie (v0.12.7). Statistical analysis was done using R version 4.0.1. We merged the gene expression levels which were calculated by RSEM48 for MGH170 and MGH229 with the ones calculated for the reference samples from Tirosh 2016 (downloaded from https://singlecell.broadinstitute.org/single_cell). Analysis was done mainly using the R package scandal which is freely available at https://github.com/dravishays/scandal.  Gene expression levels were quantified as TPM (transcript-per-million reads).
Assembly: GRCh38 for Homo sapiens, mm10 for Mus musculus
Supplementary files format and content: tsv

source_name: Mouse cell line single cell, IDHmutant mouse glioma cell

extract_protocol:
Fresh specimens were mechanically dissociated with a disposable, sterile scalpel and further enzymatically dissociated into single cell suspensions using the enzymatic brain dissociation kit (papain-based) from Miltenyi Biotec as previously reported. Tumor cells were blocked in 1% bovine serum albumin in phosphate-buffered saline solution (1% BSA / PBS). Cell suspensions were subsequently stained for flow cytometry for 30 min at 4 °C using antibodies specific for CD45 [REA747]-VioBlue and CD3 [BW264/56]-PE from Miltenyi Biotec. Cells were washed with cold PBS, and then incubated for 15 min in 1.5 mL of 1% BSA / PBS containing 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies). Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter; CD3-PE, 585/42 filter), 640nm (TO-PRO-3, 670/14 filter), and 405 nm (CD45-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3. We sorted individual, viable, CD45+CD3- and CD45+CD3+ immune, and CD45- non-immune single cells into 96-well plates containing cold TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80 °C prior to whole transcriptome amplification, library preparation and sequencing. Frozen tumor tissue (approximately 5mm x 5mm x 5mm) was placed into a well of a 6-well plate (Corning, Cat. No. CLS3516-50EA) containing 1 ml of CST buffer and processed on ice. Tumor tissue was chopped for 10 minutes using Noyes Spring Scissors (Fine Science Tools, Cat. No. 15514-12). The sample was then filtered through a 40 um cell strainer (Fisher Scientific, Cat. No. 22363547) and the well and filter were washed with an additional 1 ml of CST buffer. The total volume was then brought up to 5 ml with 3 ml of ST buffer and the sample was centrifuged in a 15 ml conical tube at 4°C for 5 minutes at 500 g. The supernatant was removed and the pellet was resuspended in 100 ul ST buffer. The sample was then filtered through a 35 um cell strainer (Falcon, Cat. No. 352235). Nuclei suspension was counted using disposable C-Chip Hemocytometers (INCYTO, Cat. No. DHCN012). Single-nuclei were loaded on 10x genomics or stained by Ruby (ThermoFisher, V10309) and sorted into 96 well plates. IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks.  The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and  640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
RNA from single cells or single nucleus was first purified with Agencourt RNAClean XP beads (Beckman Coulter). B65Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli 2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 768 cells with unique barcodes were combined and sequenced using a NextSeq sequencer (Illumina). Multi-omics library (DNA methylome and transcriptome) was generated based on the Smart-RRBS protocol (Chaligne et al, 2021).

tag: treatment (idhi)

value: No


title: PRS3


title: PRS4


title: APP/PS1_12M_rep2


title: Exp-2

city: Seoul

first: Jeongbin

last: Park

state: Not US or Canada

address: 23, Sinhyeon-ro 38beon-gil, Siheung-si, Gyeonggi-do, 14957, Rep. of KOREA

department: Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University

description: Fresh frozen Spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
We used spaceranger mkref in Space Ranger (version 2.0.1) pipeline to combine the human reference, GRCh38, with the mouse reference, mm10.
We ran spaceranger count on each sample to generate the processed ST cDNA library against a combined human and mouse reference genome to detect human transcripts from the administered cells in mouse tissues, if any.
Assembly: GRCh38 and mm10
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

organism:
Homo sapiens
Mus musculus

source_name: Lung Fibrosis Treated with hMSCs

growth_protocol: Normal bone marrow derived hMSC was prepared from Lonza™. We prepared five male C57BL/6 mice, each 9 weeks old. The first class was a normal mouse (labeled ‘Nor’). The second class was two mice with lung fibrosis, serving as a control (labeled ‘Con’ or ‘Con-2’). The third class was two mice with lung fibrosis, but they also received an injection of hMSC through their tail veins, making them the experimental group (labeled ‘Exp’ or ‘Exp-2’). Lung fibrosis was triggered in both the control (‘Con’ or ‘Con-2’) and experimental (‘Exp’ or ‘Exp-2’) groups by injecting bleomycin for 3 weeks before they were sacrificed.

extract_protocol:
Optimal cutting temperature (OCT) blocks (Scigen 4586, USA) were made according to the Visium Spatial Protocols – Tissue Preparation Guide (Document CG000240). The OCT blocks from the experimental group were created 6 hours after injecting human stem cells. For each sample of all the classes, two tissue slices were acquired from each OCT mold. One was prepared for H&E staining, and the other was kept as a fresh frozen slice for Visium ST library.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer’s construction.

treatment_protocol: Bone marrow-derived hMSC was injected intravenously into the ‘Exp’ and ‘Exp-2’ samples, which were then sacrificed 6 hours later.

value: Lung Fibrosis Treated with hMSCs

tag: treatment

value: Therapy with Normal bone marrow derived hMSC, prepared from Lonza™


title: GB1-2


title: Exp


title: GB1-4


title: C57_6M_rep1

description: gene expression in the hippocampus of 6months old C57 mice


title: APP/PS1_12M_rep1


title: APP/PS1_3M_rep3

description: gene expression in the hippocampus of 3months old APP/PS1 mice


title: APP/PS1_6M_rep1

description: gene expression in the hippocampus of 6months old APP/PS1 mice


title: APP/PS1_3M_rep1


title: PmB treatment biol rep 2 for strain E104107

city: Belfast

first: Inmaculada

last: Garcia-Romero

address: 97 Lisburn Rd

country: United Kingdom

institute: QUB

data_processing:
To assure high sequence quality, reads were quality and adapter-trimmed via Cutadapt v2.5
The reads were aligned to Enterobacter cloacae strain E105227 and E104107 using segemehl58 v.0.2.0 (3) with an accuracy cutoff of 95%.
READemption57 v.0.4.5 gene quanti was used to quantify aligned reads on the overlapping genomic features. For this, we supplied annotations (CDS, ncRNA, rRNA, tmRNA and tRNA) in GFF format.
For annotation-based identification of enriched genomic regions we used DESeq2 version 1.24.0
Assembly: Whole genome sequence used for mapping is deposited in a public database. The accession number will be added as soon as it is issued  The annotation for the same is available in the associated manuscript.
Supplementary files format and content: CSV:Read count table for strain E104107
Supplementary files format and content: CSV: Read count table for strain E105227

organism: Enterobacter cloacae

source_name: bacteria

growth_protocol: Bacteria were grown in LB media in presence or absence of PmB

extract_protocol:
RNA was harvested using Direct-zol™ RNA MiniPrep Plus w/ Zymo-Spin™ IIICG Columns (Capped) w/ TRI Reagent™
The RIN for all samples was ≥ 8.0. DNA libraries suitable for sequencing were prepared from 100 ng of total RNA, using TruSeq Stranded Total RNA library preparation kit combined with Illumina Ribo-Zero Plus for rRNA Depletion

tag: strain

value: bacteria

value: WT

value: PmB treatment


title: APP/PS1_6M_rep2


title: DMSO_P1_F10_S166, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: DMSO_P1_G02_S170, Smart-seq2 (multi-omics)


title: Control biol rep 1 for strain E104107

value: control


title: Cerebral cortex, acupuncture + thrombolytic, 2

city: Nanjing

first: Zhihui

last: Zhang

state: Jiangsu

address: 138 Xianlin Rd

institute: Nanjing University of Chinese Medicine

data_processing:
After low-quality filtering, the sequences are then filtered using sortmerna v4.3.4 for rRNA. Next, STAR v2.7.10a is used to align the filtered sequence data to a reference genome (Rattus norvegicus mRatBN7.2). Then, several alignment evaluation tools such as RSeQC v4.0.0, QualiMap v2.2.2, featureCounts v2.0.1, and Preseq v3.1.1 are used to assess the quality of the alignment. Using Salmon v1.9.0, RNA quantification is performed on the aligned results. The transcripts and their annotations are referenced to the ENSEMBL 108 database for reference genes and transcripts levels of mRNA and lncRNA expression quantification is obtained from quantitative analysis. The results are provided at the gene and transcript levels for each sample.
Assembly: Rattus norvegicus mRatBN7.2
Supplementary files format and content: count matrix

organism: Rattus norvegicus

source_name: Cerebral cortex

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Cerebral cortex

tag: Sex

value: male

value: acupuncture + thrombolytic


title: DMSO_P1_F12_S168, Smart-seq2 (multi-omics)


title: PRS2


title: DMSO_P1_F11_S167, Smart-seq2 (multi-omics)


title: PmB treatment biol rep 3 for strain E104107


title: APP/PS1_3M_rep2


title: Cerebral cortex, acupuncture + thrombolytic, 1


title: Cerebral cortex, acupuncture + thrombolytic, 3


title: Control biol rep 3 for strain E104107


title: PmB treatment biol rep 2 for strain E105227


title: DMSO_P1_F09_S165, Smart-seq2 (multi-omics)


title: Control biol rep 2 for strain E104107


title: PmB treatment biol rep 3 for strain E105227


title: PmB treatment biol rep 1 for strain E105227


title: DMSO_P1_F08_S164, Smart-seq2 (multi-omics)


title: DMSO_P1_F07_S163, Smart-seq2 (multi-omics)


title: Control biol rep 3 for strain E105227


title: PmB treatment biol rep 1 for strain E104107


title: Cerebral cortex, rt-PA thrombolytic, 3

value: rt-PA thrombolytic


title: DMSO_P1_F06_S162, Smart-seq2 (multi-omics)


title: Control biol rep 1 for strain E105227


title: DMSO_P1_F05_S161, Smart-seq2 (multi-omics)


title: Control biol rep 2 for strain E105227


title: S_LA_EAT_3, miRNA-seq

city: Wuhan

first: wang

last: xuewen

address: 238 Jiefang Road, Wuhan 430060, China

department: Department of Cardiology

institute: Renmin Hospital of Wuhan University

description: EAT Exosomes miRNA_TPM.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI.
The de-duplicated consensus sequences were mapped to CanFam 3.1 using STAR software (version 2.5.3a)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）
Assembly: CanFam 3.1
Supplementary files format and content: tab-delimited text files include RPKM values/TPM values for each Sample

organism: Canis lupus familiaris

source_name: Exosome from epicardial fat in the left atrium

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

tag: breed

value: beagle

value: sham operation


title: S_LA_EAT_2, miRNA-seq

description: EAT Exosomes miRNA_TPM.txt

value: Exosome from epicardial fat in the left atrium


title: Cerebral cortex, rt-PA thrombolytic, 2


title: P_LA_EAT_3, miRNA-seq

description: EAT Exosomes miRNA_TPM.txt

value: rapid atrial pacing for 2 weeks


title: Sham Hip-3, mRNA-seq

description: Hippocampus All_samples_rpkm.txt

value: hippocampus


title: S_LA_EAT_1, miRNA-seq

description: EAT Exosomes miRNA_TPM.txt


title: DMSO_P1_F03_S159, Smart-seq2 (multi-omics)

value: No


title: Cerebral cortex, rt-PA thrombolytic, 1


title: DMSO_P1_F04_S160, Smart-seq2 (multi-omics)


title: Cerebral cortex, model, 1

value: model


title: Sham Hip-1, mRNA-seq

description: Hippocampus All_samples_rpkm.txt


title: DMSO_P1_E10_S154, Smart-seq2 (multi-omics)


title: Cerebral cortex, model, 3


title: Cerebral cortex, sham, 3

value: sham


title: P_LA_EAT_2, miRNA-seq

description: EAT Exosomes miRNA_TPM.txt


title: Pacing Hip-3, mRNA-seq

description: Hippocampus All_samples_rpkm.txt


title: Cerebral cortex, model, 2


title: P_LA_EAT_1, miRNA-seq

description: EAT Exosomes miRNA_TPM.txt


title: Pacing Hip-1, mRNA-seq

description: Hippocampus All_samples_rpkm.txt


title: DMSO_P1_E12_S156, Smart-seq2 (multi-omics)


title: APP/PS1_6M_rep3


title: Sham Hip-2, mRNA-seq

description: Hippocampus All_samples_rpkm.txt


title: Cerebral cortex, sham, 1


title: DMSO_P1_E06_S150, Smart-seq2 (multi-omics)


title: LM2Tr, fungal biomass, low-melanin necromass, rep2

city: Saint Paul

first: Jonathan

last: Schilling

state: Minnesota

address: 1445 Gortner Avenue

department: Plant and Microbial Biology

institute: University of Minnesota

data_processing:
Raw data were processed with Collection of Hierarchical UMII-RIS Pipelines (CHURP; v0.2.2; Baller et al., 2019).
Kallisto v0.48.0 (Bray et al., 2016) was used to build the index and quantify transcripts
DESeq2 v1.42.0 (Love et al., 2014) was used to perfom differential gene expression analysis
Assembly: Trichoderma_reesei_rut_c_30_gca_000513815.TrireRUTC30_1.cdna.all.fa.gz
Supplementary files format and content: csv files containing raw counts for each sample

organism: Trichoderma reesei

growth_protocol: Trichoderma reesei was routinely maintained on malt extract agar plates.

extract_protocol:
RNA was extracted using TRIzol and PureLink RNA mini kit
NEBNext Ultra II RNA Library Prep kit

treatment_protocol: Three treatments were used: 1. Highley’s medium supplemented with 1% (w/v) glucose, 2. Highley’s medium with 0.45% (w/v) low-melanin necromass, 3. Highley’s medium with 0.45% high-melanin necromass

tag: time

value: 7 days

value: Low-melanin necromass


title: DMSO_P1_E05_S149, Smart-seq2 (multi-omics)


title: DMSO_P1_E09_S153, Smart-seq2 (multi-omics)


title: bLR_RatL09_B3_HC__NIL_NIL

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

data_processing:
Within the MBNI Analysis Hub (“Ahub”: https://ahub.mbni.org) pipeline, RNA-Seq data was aligned using the STAR algorithm (2.7.0f, Encode parameter: unique hit only) to genome assembly Rnor6
Reads were summarized into counts per transcript using featureCounts (v1.6.4) and Ensembl 96 annotation.
Primary quality control: Within the Ahub pipeline, principal components analysis was used to identify extreme outlier samples, which were presumed to reflect unknown sources of technical variation (NACC: 2 samples, HC: 6 samples). These samples did not represent any particular treatment group or processing batch and were removed before further analysis was performed.
Secondary quality control and normalization was performed in Rstudio (v.1.0.153, R v. 3.4.1) for the NACC and HC datasets independently. Only one NACC sample was removed at this stage due to a notably low distribution of log2 counts per million (cpm).
Assembly: Rnor6
Supplementary files format and content: The processed data files are tab-delimited text files that include the read counts per transcript (Rnor6 with Ensembl 96 annotation) for each sample that survived the first level of quality control. There is a separate file for the Nucleus Accumbens samples (NAcc_remove2samples_gene_featureCounts_counts.txt) and Hippocampal samples (Hippocampus_remove6samples_gene_featureCounts_counts.txt) because they were processed in separate batches.

source_name: hipppocampus (HC)

growth_protocol: The male bred Low-Responder (bLR) Sprague-Dawley rats used in the RNA-Seq experiment were from the University of Michigan MBNI colony (generations F49, F53, F56). Litters were culled on postnatal day 1 (P1) to even sex ratios (minimum litter size: 3M/3F, maximum: 6M/6F). Animals were housed on a 12:12 hour light:dark cycle (lights on: 7am) with ad libitum access to water and food. Litters were weaned at P21 and males were pair- or triple-housed with littermates.

extract_protocol:
Tissue and blood collection: On P68, animals habituated to a new room (>30 minutes), then were removed to the sacrifice room and immediately decapitated without anaesthesia. Trunk blood was collected in EDTA tubes and placed onto ice before centrifugation (3000 rpm, 4oC) for 10 minutes. Plasma supernatant was stored at -80oC. Brains were removed within 2 minutes of death, flash-frozen (-30oC), and stored at -80oC.  All brains were hemi-sected (groups counter-balanced by side), and one half dissected within a cryostat (-20oC); the NAcc (+1.5mm to +1mm Anterior-Posterior [46]) was extracted by 2mm hole-punch, and whole dorsal HC (-3mm to -4mm Anterior-Posterior [46]) extracted using dissection tools.   RNA extraction: Nucleotides were extracted from NACC and HC tissue using Qiagen AllPrep DNA RNA miRNA Universal Kit 50. Extracted RNA was evaluated for total concentration and quality using a Nanodrop spectrophotometer (concentration range: 285-432 ng/ul, 260/280 ratio range: 1.61-1.80).
Samples were processed by the University of Michigan DNA Sequencing Core (https://brcf.medicine.umich.edu/cores/dna-sequencing/). RNA integrity (RIN) was assessed using the TapeStation automated sample processing system (Agilent, Santa Clara, CA). Samples with RINs<8 were excluded. A DNA library targeting polyadenylated transcripts was constructed for each sample (100ng total RNA) with the KAPA hyper mRNA stranded library prep kit (Roche, catalogue# KK8581) in a 12-cycle PCR. Final cDNA libraries were checked for quality by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalogue# KK4835, Kapa Biosystems, Wilmington MA).

treatment_protocol: Adolescent Enrichment: At postnatal day 35 a subset of animals was assigned to a group to receive Social and Environmental Enrichment (EE). Enriched cages consisted of a large (50 x 40 x 50cm) cage with three separate levels connected by mesh ramps, and contained various other objects that were added to the cage and moved around over the duration of enrichment. EE groups spent an hour a day in these cages, 5 days a week from P35 to P60. All animals from one litter were placed into the same EE cage such that the number of animals present during each session was between 4 and 6, depending on litter size. The comparison group (NIL) received standard housing from P35-P60.  Repeated social stress:  From P61-64, the experimental bHR/bLR rats were each introduced individually to a Long-Evans aggressor’s cage to experience a daily 15-minute social stress episode. The bHR/bLR intruder could move freely throughout the cage until an aggressive interaction (pinning). Intruders were then placed into a protective wire mesh container (10x10x15cm) within the Long-Evans cage for the remainder of the trial.  Each day, each bLR/bHR intruder was exposed to a different Long-Evans aggressor. Any rat that sustained physical wounds during social defeat was excluded from the study. Experimental bHR/bLR rats that were in the no defeat group (“NIL”) were placed in a clean, empty novel cage within the same testing room and allowed to move freely for the 15-minute period.   Behavioural testing: On P65-66, experimental animals underwent a social interaction test consisting of two 5-minute trials on consecutive days (Day 1: habituation, Day 2: testing). The testing arena was a white Plexiglass open field (100x100cm). The bHR/bLR rats were placed into the centre of the testing field on both days. On Day 2, there was a caged novel stimulus male Long-Evans rat (“target”) present, with zones of the open field predefined as target, interaction, and social avoidance zones. A video tracking system (Ethovision XT 11.5, Noldus Information Technology) calculated the percent time the bHR/bLR rats spent in each zone. On P67, animals underwent the Elevated Plus Maze (EPM). The EPM consists of four intersecting black Plexiglass arms (45cmx12cm) shaped like a cross, elevated 70cm from the floor. Two opposite arms are enclosed (45cm walls) and two remain open; at the intersection a square platform (12x12cm) allows access to all arms. During the five-minute test, the room was dimly lit (40 lux) and animals’ behaviour monitored using a video tracking system (Ethovision XT 11.5, Noldus Information Technology ) that recorded latency to enter the open arm, the amount of time spent in the arms and centre square.

tag: rat

tag: hemisphere

value: left

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

value: no social defeat stress (NIL)

tag: adolescent environmental enrichment

value: standard housing (NIL)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control

value: Good


title: DMSO_P1_E03_S147, Smart-seq2 (multi-omics)

tag: tissue

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)


title: TRG2, fungal biomass, glucose, rep2

tag: strain

tag: time

tag: treatment

value: Glucose


title: Pacing Hip-2, mRNA-seq

description: Hippocampus All_samples_rpkm.txt

tag: breed

value: beagle


title: Cerebral cortex, sham, 2

value: Cerebral cortex

tag: Sex

value: male


title: DMSO_P1_E08_S152, Smart-seq2 (multi-omics)


title: Burdock root

first: Huichen

last: Song

address: Qixia District, Xianlin Road No.163

institute: Nanjing university

data_processing:
The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers [5]. The expression formula is Expression = C * 1000000/ T, C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
Assembly: ASM2352574v1
Supplementary files format and content: tab-delimited text file includes small RNA expression levels

organism: Arctium lappa

source_name: root

extract_protocol:
RNA was harvested using miRNeasy kit(04053228006244).
RNA libraries were prepared for sequencing using standard BGI protocols

value: root


title: LAMN PM 4

city: Irvine

first: Eric

last: Hanse

state: CA

address: 3119 McGaugh Hall

institute: University of California Irvine

data_processing:
Trimmomatic
FastQC
STAR alignment
FeatureCounts
DESEQ2
Assembly: GRCh38.p13.genome.fa
Supplementary files format and content: FeatureCounts of each individual sample with gene names
Supplementary files format and content: DESEQ2 results LAMN versus Adenocarcinoma derived peritoneal metastatic tumors

organism: Homo sapiens

source_name: Appendecial peritoneal metastasis

growth_protocol: resected tissue

extract_protocol: Trizol-total RNA

treatment_protocol: Homogenized

value: Appendecial peritoneal metastasis

tag: cell line

value: tissue

tag: cell type

value: cancer

tag: genotype

value: Unknown

tag: subject id

value: Patient 98


title: DMSO_P1_E07_S151, Smart-seq2 (multi-omics)

value: No


title: bLR_RatL11_A2_HC__EE_SD

tag: rat

tag: hemisphere

value: left

tag: animal strain

tag: social defeat stress

value: social defeat stress (SD)

tag: adolescent environmental enrichment

value: social and environmental enrichment (EE)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)


title: TrHM1, fungal biomass, high-melanin necromass, rep1

tag: strain

tag: time

value: 7 days

tag: treatment

value: High-melanin necromass


title: TrHM2, fungal biomass, high-melanin necromass, rep2


title: DMSO_P1_E02_S146, Smart-seq2 (multi-omics)

tag: tissue

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)


title: LM3Tr, fungal biomass, low-melanin necromass, rep3

value: Low-melanin necromass


title: bLR_RatKH_L07_B1_HC__EE_NIL

tag: rat

value: KH L07 B1

tag: hemisphere

value: right

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

value: no social defeat stress (NIL)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control

value: Good


title: TRG3, fungal biomass, glucose, rep3

value: Glucose


title: LAMN PM 3

value: Appendecial peritoneal metastasis

tag: cell line

value: tissue

tag: cell type

value: cancer

tag: genotype

tag: subject id

value: Patient 86


title: LM1Tr, fungal biomass, low-melanin necromass, rep1

tag: strain

tag: time


title: CRC PM 2

source_name: Adenocarcinoma peritoneal metastasis

tag: tissue

value: Adenocarcinoma peritoneal metastasis

value: Unknown

tag: treatment

value: Patient 66


title: DMSO_P1_D10_S142, Smart-seq2 (multi-omics)

tag: treatment (idhi)

value: No


title: CRC PM 1

value: Patient 63


title: TRG1, fungal biomass, glucose, rep1

value: 7 days


title: bLR_RatKH_L07_D3_HC__EE_SD

tag: rat

value: KH L07 D3

tag: hemisphere

value: left

value: social defeat stress (SD)

tag: adolescent environmental enrichment

value: social and environmental enrichment (EE)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)


title: TrHM3, fungal biomass, high-melanin necromass, rep3

tag: strain

tag: time

value: High-melanin necromass


title: bLR_RatKH_L07_D2__HC__EE_SD

value: KH L07 D2

value: right

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control

value: Good


title: CRC PM 4

tag: tissue

tag: cell line

value: tissue

tag: cell type

value: cancer

tag: genotype

tag: treatment

tag: subject id

value: Patient 89


title: bLR_RatL11_A3_HC__EE_SD

tag: rat

tag: hemisphere

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)


title: DMSO_P1_D08_S140, Smart-seq2 (multi-omics)

tag: tissue

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)


title: bLR_RatKH_L07_D1_HC__EE_SD

value: KH L07 D1

tag: animal strain

tag: social defeat stress

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: DMSO_P1_E01_S145, Smart-seq2 (multi-omics)

value: No


title: bLR_RatL11_A1_HC__EE_SD

tag: rat

tag: hemisphere

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice


title: CRC PM 3

value: Adenocarcinoma peritoneal metastasis

tag: cell line

tag: cell type

tag: genotype

value: Unknown

tag: treatment

tag: subject id

value: Patient 83


title: DMSO_P1_D12_S144, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: LAMN PM 2

value: Appendecial peritoneal metastasis

value: Patient 78


title: bLR_RatKH_L07_C2_HC__EE_SD

value: KH L07 C2

value: left

tag: animal strain

tag: social defeat stress

value: social defeat stress (SD)

value: social and environmental enrichment (EE)

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)


title: bLR_RatKH_L07_B2_HC__EE_NIL

tag: rat

value: KH L07 B2

tag: hemisphere

value: bred Low Responder (bLR)

value: no social defeat stress (NIL)

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: bLR_RatKH_L07_A2_HC__EE_NIL

value: KH L07 A2

tag: animal strain

tag: social defeat stress

tag: date of dissection

tag: date of rna extraction


title: DMSO_P1_D05_S137, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: bLR_RatKH_L07_C1_HC__EE_SD

value: KH L07 C1

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

value: Good


title: Patid78

city: COLUMBUS

first: Deedra

middle: R

last: Nicolet

state: OH

address: 1800 Cannon Drive, Rm 1250H

department: CCC

institute: The Ohio State University

data_processing:
RNA-seq data were processed using the EnFusion ensemble approach of seven fusion detection algorithms
Transcripts per million (TPM) values were generated from paired-end RNA sequence data using Salmon with bootstrapping set to 100
Assembly: Homo sapiens GRCh38.p12
Supplementary files format and content: Salmon TPM

source_name: BM/pB

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq Stranded Total with Rebo Zero Gold library preparation kit following manufacturer's protocols.
Tumor derived RNA was subjected to 0.8x SPRI beadcleanup and size selection prior to DNase treatment and ribodepletion prior to using the NEBNext Ultra II Directional kit preparation. The library was constructed for whole transcriptome sequencing (RNA-seq). Paired-end 151-bp reads were generated on the Illumina NovaSeq (Illumina, Inc.)

value: BM/pB

tag: cell type

value: mononuclear leukocytes

tag: treatment

value: cytotoxic induction therapy with cytarabine/daunorubicin


title: DMSO_P1_D09_S141, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell

value: No


title: LAMN PM 1

value: Appendecial peritoneal metastasis

tag: cell line

value: tissue

value: cancer

tag: genotype

value: Unknown

tag: subject id

value: Patient 52


title: Patid77


title: Patid70


title: Patid76


title: Patid75


title: DMSO_P1_D07_S139, Smart-seq2 (multi-omics)


title: Patid67


title: Patid66


title: DMSO_P1_D02_S134, Smart-seq2 (multi-omics)


title: Patid74


title: Patid73


title: Patid72


title: Patid65


title: Patid64


title: bLR_RatL11_B1_HC__EE_NIL

tag: rat

tag: hemisphere

value: left

tag: animal strain

tag: adolescent environmental enrichment

value: social and environmental enrichment (EE)

tag: generation

tag: family

tag: date of sacrifice

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: DMSO_P1_D04_S136, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: Patid69

tag: cell type

tag: treatment


title: DMSO_P1_D03_S135, Smart-seq2 (multi-omics)


title: Patid68


title: bLR_RatKH_L07_A1_HC__EE_NIL

value: KH L07 A1

value: right

value: bred Low Responder (bLR)

tag: social defeat stress

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: DMSO_P1_C10_S130, Smart-seq2 (multi-omics)


title: bLR_RatL11_B2_HC__EE_NIL

tag: rat

tag: hemisphere

tag: animal strain

value: no social defeat stress (NIL)

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: social interaction (percent time in interaction zone during social interaction test)


title: bLR_RatL08_D2_HC__NIL_SD

tag: social defeat stress

value: social defeat stress (SD)

value: standard housing (NIL)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control

value: Good


title: bLR_RatL11_B3_HC__EE_NIL

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio


title: Patid60

tag: tissue

value: BM/pB

tag: cell type

value: mononuclear leukocytes

tag: treatment

value: cytotoxic induction therapy with cytarabine/daunorubicin


title: DMSO_P1_C12_S132, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)

value: No


title: bLR_RatL08_D1_HC__NIL_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: adolescent environmental enrichment

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: Patid71


title: DMSO_P1_C08_S128, Smart-seq2 (multi-omics)


title: bLR_RatL08_C1_HC__NIL_SD

tag: social defeat stress

tag: generation

tag: family

tag: date of sacrifice

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: Patid55

tag: tissue

tag: cell type

tag: treatment


title: DMSO_P1_C11_S131, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: Patid61


title: Patid59


title: DMSO_P1_C09_S129, Smart-seq2 (multi-omics)


title: Patid49


title: DMSO_P1_C01_S121, Smart-seq2 (multi-omics)


title: bLR_RatL08_A1_HC__NIL_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: adolescent environmental enrichment

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio


title: Patid47


title: Patid56


title: Patid58


title: DMSO_P1_B12_S120, Smart-seq2 (multi-omics)


title: bLR_RatL08_C2_HC__NIL_SD

tag: social defeat stress

tag: generation

tag: family

tag: date of sacrifice

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: bLR_RatL09_B2_HC__NIL_NIL

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: Patid57

tag: tissue

tag: cell type

tag: treatment


title: Patid53


title: DMSO_P1_B11_S119, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: Patid44


title: Patid63


title: DMSO_P1_C07_S127, Smart-seq2 (multi-omics)


title: Patid54


title: Patid45


title: bLR_RatL09_B1_HC__NIL_NIL

tag: rat

tag: hemisphere

tag: animal strain

tag: adolescent environmental enrichment

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio


title: Patid43


title: Patid62


title: DMSO_P1_C05_S125, Smart-seq2 (multi-omics)


title: Patid52


title: bLR_RatL08_B1_HC__NIL_SD

tag: social defeat stress

tag: generation

tag: family

tag: date of sacrifice

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: bLR_RatL09_A1_HC__NIL_NIL

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: Patid51

tag: tissue

tag: cell type

tag: treatment


title: bLR_RatL10_A3_HC__NIL_NIL

tag: rat

tag: hemisphere

tag: animal strain

tag: adolescent environmental enrichment

tag: date of dissection

tag: date of rna extraction

tag: rna concentration


title: DMSO_P1_B07_S115, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: DMSO_P1_C04_S124, Smart-seq2 (multi-omics)


title: Patid37


title: Patid50


title: Patid48


title: bLR_RatL10_A2_HC__NIL_NIL

tag: social defeat stress

tag: generation

tag: family

tag: date of sacrifice

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)


title: Patid36

tag: tissue

tag: cell type

tag: treatment


title: Patid35


title: Patid46


title: Patid32


title: bLR_RatL08_B2_HC__NIL_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: bLR_RatL08_A2_HC__NIL_SD

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of dissection

tag: date of rna extraction

tag: rna concentration


title: bLR_RatL08-2_C1_NACC__EE_SD

source_name: nucleus accumbens (NACC)

tag: date of sacrifice

tag: rna 260 280 ratio

tag: distance traveled (open field habituation)


title: Patid30

tag: tissue

tag: cell type

tag: treatment


title: DMSO_P1_B03_S111, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: Patid42


title: DMSO_P1_B10_S118, Smart-seq2 (multi-omics)


title: Patid29


title: Patid28


title: bLR_RatL09_A2_HC__NIL_NIL

tag: rat

tag: hemisphere

tag: animal strain

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: Patid27


title: DMSO_P1_B01_S109, Smart-seq2 (multi-omics)


title: DMSO_P1_B09_S117, Smart-seq2 (multi-omics)


title: Patid41


title: Patid40


title: DMSO_P1_A12_S108, Smart-seq2 (multi-omics)


title: bLR_RatL08-2_A2_NACC__EE_SD

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of dissection

tag: date of rna extraction

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: bLR_RatL08-2_A1_NACC__EE_SD

tag: date of sacrifice

tag: rna concentration

tag: rna 260 280 ratio

tag: distance traveled (open field habituation)


title: Patid23

tag: tissue

tag: cell type

tag: treatment


title: DMSO_P1_A11_S107, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: Patid39


title: MDA-MB-231 IFN-β  biol rep2

city: Groningen

first: Marcel

last: van Vugt

state: Netherlands

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and BclConvert v4.2.4
Sequence reads were trimmed to remove possible adapter sequences and filtered on low-quality bases using fastp v0.23.2.
The trimmed reads were mapped to the human GRCh38.p13
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v2.0.2.
To enable comparison of gene/transcript expression across all samples outside of the context of differential expression analysis, FPKM and CPM values were calculated with Cufflinks v2.2.1
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: HCC38 and MDA-MB-231 cells were maintained in RPMI-1640 medium and DMEM (1 g/L glucose) respectively. All growth media were supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin (100 units/mL). Both cell lines were cultured at 37 °C supplied with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina"

treatment_protocol: HCC38 and MDA-MB-231 cell lines were treated with with interferon-β (400 IU/mL) for 48 hours.

tag: cell line

tag: genotype

value: WT

value: IFN-Beta


title: DMSO_P1_B08_S116, Smart-seq2 (multi-omics)


title: bLR_RatL08-2_B1_NACC__EE_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: Patid38


title: bLR_RatL08-1_C2_NACC__EE_NIL

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: DMSO_P1_B06_S114, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: DMSO_P1_A09_S105, Smart-seq2 (multi-omics)


title: MDA-MB-231 biol rep3

tag: cell line

tag: genotype

tag: treatment

value: untreated


title: Patid34

tag: cell type


title: bLR_RatL10_A1_HC__NIL_NIL

tag: rat

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: Patid33


title: DMSO_P1_B05_S113, Smart-seq2 (multi-omics)


title: MDA-MB-231 IFN-β  biol rep3


title: bLR_RatL08-2_C2_NACC__EE_SD

value: left

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: bLR_RatL08-1_B2_NACC__EE_NIL

tag: rat

tag: hemisphere

tag: animal strain

tag: social defeat stress

value: social and environmental enrichment (EE)


title: Patid31

tag: tissue

tag: cell type

tag: treatment


title: DMSO_P1_B04_S112, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: bLR_RatL08-1_A2_NACC__EE_NIL

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: rna 260 280 ratio

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: DMSO_P1_A05_S101, Smart-seq2 (multi-omics)


title: bLR_RatL08-2_B2_NACC__EE_SD

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: DMSO_P1_B02_S110, Smart-seq2 (multi-omics)


title: Patid26


title: DMSO_P1_A08_S104, Smart-seq2 (multi-omics)


title: hCNCC_TCF7L2_rep1

city: Guangzhou

first: Xu

last: Xiaopeng

address: 96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District

institute: Guangzhou National Laboratory

library_source: genomic

data_processing:
CUT&RUN sequencing data were analyzed employing the CUT&RUNTools 2.0 pipeline (https://github.com/fl-yu/CUT-RUNTools-2.0). For histone peak calling, the fragment size filter was deactivated, while for TFs, fragments larger than 120 bp were filtered out. Normalized bigwig files were generated using an alignment scale factor based on spike-in reads from E. coli K12 strain MG1655
Assembly: hg38/GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: H9-derived cranial neural crest cells

extract_protocol:
The CUT&RUN assay was conducted in hCNCCs using the ChIC/CUT&RUN Kit (EpiCypher, catalog no. 14-1048). Approximately 500,000 cells were harvested using Accutase and subsequently incubated with activated ConA Beads for 10 minutes at room temperature. Primary antibodies were then added to each 50 µL reaction: IgG (EpiCypher, 13-0042k, 0.5 µg), H3K27ac (Active Motif, 39133, 0.5 µg), TCF7L2 (Cell Signaling, 2569S, 1 µg), and the mixture was incubated overnight on a nutator at 4°C. On the second day, pAG-MNase and cold calcium chloride were used to activate the cleavage of target DNA. E. coli Spike-in DNA (0.1 ng) was also added for normalization in downstream analyses. DNA purification involved phenol/chloroform extraction and ethanol precipitation.
Library preparation for histone proteins was performed using the CUT&RUN Library Prep Kit (EpiCypher, 14-1001). For TFs, modified procedures, as previously reported (https:// doi.org/10.17504/protocols.io.bagaibse), were employed to enhance the preservation of small DNA fragments

tag: cell line

value: H9-derived cranial neural crest cells

value: Stem cells


title: Patid25

tag: tissue


title: Patid24

tag: cell type


title: hCNCC_TCF7L2_rep2


title: hCNCC_H3K27ac_rep1


title: hCNCC_H3K27ac_rep2


title: DMSO_P1_A03_S99, Smart-seq2 (multi-omics)


title: HCC38 biol rep2

tag: genotype

tag: treatment


title: MDA-MB-231 IFN-β  biol rep1


title: bLR_RatL08-1_A1_NACC__EE_NIL

tag: rat

tag: hemisphere

value: right

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

tag: adolescent environmental enrichment

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: hCNCC_IgG_rep2


title: hCNCC_IgG_rep1


title: AGI881_P1_H12_S96, Smart-seq2 (multi-omics)

tag: treatment (idhi)

value: Yes


title: CD138hi, bone marrow, P0263-P0383, ADT-HTO

city: Boston

first: Duane

middle: R.

last: Wesemann

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

description:
ADT/HTO
The processed files for this sample are linked to the corresponding GEX sample

library_source: other

data_processing:
CellRanger count and vdj to process raw fastq files into a set of seven files per each run: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv v3.1.0 (BRI-531-532-533), v6.1.1 (BRI-1382-1383-1384), v7.0.1 (FC7696), v7.1.0 (other libraries)
Assembly: GRCh38-3.0.0 (BRI-531-532), GRCh38-2020-A (other libraries)
Supplementary files format and content: CellRanger count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger vdj output files: all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: Bone marrow

extract_protocol:
Single cells after sorting were encapsulated in Gel beads in Emulsion (GEM) using the 10X Controller with a Chromium Next GEM Single Cell 5' Kit v2, Chromium Single Cell Human BCR Amplification Kit, and Chromium 5’ Feature Barcode Kit.
The CITE-seq and hashing protocol described by Stoeckius et al was used to generate an antibody-derived tag  (ADT) sequencing library containing hashtag oligo tags and surface protein tags, and a 5' gene expression library (Stoeckius et al., 2017). https://www.biolegend.com/en-us/protocols/totalseq-b-or-c-with-10x-feature-barcoding-technology

value: Bone marrow

value: Plasma cell

tag: participant 1_id

tag: participant 1_sex

value: Female

tag: participant 1_food_allergy_status

value: Allergic

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

value: Non-allergic

tag: library type

value: ADT/HTO

tag: hto


title: CD138hi, bone marrow, P0263-P0383, BCR

description: 5' BCR seq

molecule: other

tag: tissue

tag: cell type

value: mRNA


title: CD138hi, bone marrow, P0263-P0383, GEX

description: 5' polyA RNA


title: CD138hi, bone marrow, P0069-P0108, BCR

description: 5' BCR seq


title: bLR_RatL08-1_C1_NACC__EE_NIL

tag: rat

tag: hemisphere

value: no social defeat stress (NIL)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

value: Good


title: MDA-MB-231 biol rep2

tag: cell line

tag: genotype

value: WT

tag: treatment

value: untreated


title: CD138hi, bone marrow, P0069-P0108, ADT-HTO

tag: tissue

tag: cell type

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

tag: library type

tag: hto

value: C0251_anti-human-Hashtag-1, C0252_anti-human-Hashtag-2, C0253_anti-human-Hashtag-3, C0255_anti-human-Hashtag-5


title: MDA-MB-231 biol rep1


title: bLR_RatL09-1_A2_NACC__NIL_NIL

tag: rat

tag: hemisphere

value: left

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

value: standard housing (NIL)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: distance traveled (open field habituation)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: HCC38 IFN-β biol rep3

tag: cell line

tag: genotype

tag: treatment

value: IFN-Beta


title: AGI881_P1_H09_S93, Smart-seq2 (multi-omics)

tag: tissue

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)


title: DMSO_P1_A07_S103, Smart-seq2 (multi-omics)

value: No


title: HCC38 IFN-β biol rep1


title: HCC38 biol rep3


title: DMSO_P1_A06_S102, Smart-seq2 (multi-omics)


title: AGI881_P1_H08_S92, Smart-seq2 (multi-omics)

value: Yes


title: HCC38 biol rep1


title: WT_hCNCC_PC_HiC

data_processing:
Capture Hi-C data of human cranial neural crest cells (hCNCCs), a genome digest file for HindIII was created using hicup_digester. The HiCUP software (version 0.9.2) was then employed to generate alignment files. To prepare files for the Chicago R package (version 1.30.0), scripts such as bam2chicago.sh and makeDesignFiles.py from chicagoTools were utilized. The Chicago package produced washU_text format results, showcasing interactions between two genomic positions. Interactions with a score bigger than 5 were considered high-confidence and visualized as arcs using pygenometrack (version 3.9)
Assembly: hg19
Supplementary files format and content: tab-delimited genomic regions interacted with gene promoters

extract_protocol:
Cells were first fixed with 2% formaldehyde for 10 minutes at ambient temperature, followed by quenching with 0.2M glycine for 5 minutes. Post-fixation, cells were lysed, and endogenous nucleases were inactivated with 0.3% SDS. Chromatin was digested using 100U of HindIII (New England Biolabs), labeled with biotin-14-dCTP (Invitrogen), and then ligated using 50U of T4 DNA ligase (New England Biolabs). After reversing the cross-links, DNA was isolated using the QIAamp DNA Mini Kit (Qiagen), in strict accordance with the manufacturer's instructions. Subsequent steps involved fragmenting the DNA to 300-600 bp, end-repair, A-tailing, and adapter ligation using SureSelect adaptors. Biotinylated fragments were isolated through streptavidin-affinity pull-down and PCR amplified.
Promoter-specific Capture Hi-C was performed using the SureSelect XT Library Prep Kit ILM (Agilent Technologies), which included a custom-designed biotinylated RNA bait library and paired-end blockers. Post-capture PCR enrichment was followed by final purification of the libraries with AMPure XP beads (Beckman Coulter). Library quality was evaluated using Bioanalyzer profiles (Agilent Technologies), and high-throughput sequencing was performed on the Illumina NovaSeq 6000 platform.
promoter capture HiC

value: H9-derived cranial neural crest cells

tag: cell type

value: Stem cells


title: HCC38 IFN-β biol rep2


title: CD138hi, bone marrow, P0433, ADT-HTO

value: Bone marrow

value: Plasma cell

tag: participant 1_id

tag: participant 1_sex

value: Male

tag: participant 1_food_allergy_status

value: Allergic

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

tag: library type

tag: adt


title: bLR_RatL08-1_B1_NACC__EE_NIL

tag: rat

tag: hemisphere

value: right

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

value: no social defeat stress (NIL)

tag: adolescent environmental enrichment

value: social and environmental enrichment (EE)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: DMSO_P1_A04_S100, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: AGI881_P1_H06_S90, Smart-seq2 (multi-omics)


title: CD138hi, bone marrow, P0287-P0530, ADT-HTO

tag: cell type

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status

value: Non-allergic

tag: participant 2_id

tag: participant 2_sex

value: Female

tag: participant 2_food_allergy_status

tag: library type

value: ADT/HTO

tag: adt

value: C0050_anti-human-CD19, C0831_anti-human-CD138, C0410_anti-human-CD38, WT-Spike_Oligo-1, Omicron-Spike_Oligo-2

tag: hto


title: bLR_RatKH_L07_D1_NACC__EE_SD

tag: rat

value: KH L07 D1

tag: hemisphere

tag: animal strain

tag: social defeat stress

value: social defeat stress (SD)

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control

value: Good


title: CD138hi, bone marrow, P0287-P0530, GEX

description: 5' polyA RNA

tag: tissue

tag: cell type

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

tag: library type

value: mRNA


title: bLR_RatL12_B2_NACC__NIL_SD

tag: rat

tag: hemisphere

value: left

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

value: standard housing (NIL)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: bLR_RatL12_A2_NACC__NIL_SD

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: AGI881_P1_H11_S95, Smart-seq2 (multi-omics)

tag: tissue

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)

value: Yes


title: AGI881_P1_H10_S94, Smart-seq2 (multi-omics)


title: bLR_RatL12_A1_NACC__NIL_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: social defeat stress


title: AGI881_P1_H03_S87, Smart-seq2 (multi-omics)


title: bLR_RatL12_B1_NACC__NIL_SD

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice


title: bLR_RatL09-1_A1_NACC__NIL_NIL

tag: date of dissection

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)


title: CD138hi, bone marrow, P0069-P0108, GEX

description: 5' polyA RNA

value: Bone marrow

tag: cell type

value: Plasma cell

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status

value: Allergic

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

tag: library type


title: CD138hi, bone marrow, P0435, ADT-HTO

tag: tissue

value: Male

tag: adt


title: CD138hi, bone marrow, P0433, BCR

description: 5' BCR seq


title: bLR_RatL11_A3_NACC__EE_SD

tag: rat

tag: hemisphere

value: right

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

tag: adolescent environmental enrichment

value: social and environmental enrichment (EE)

tag: generation

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: CD138hi, bone marrow, P0287-P0530, BCR

description: 5' BCR seq

tag: cell type

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status

value: Non-allergic

tag: participant 2_id

tag: participant 2_sex

value: Female

tag: participant 2_food_allergy_status

tag: library type


title: bLR_RatKH_L07_D3_NACC__EE_SD

tag: rat

value: KH L07 D3

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)


title: CD138hi, bone marrow, P0433, GEX

description: 5' polyA RNA

tag: tissue

tag: cell type

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status


title: bLR_RatKH_L07_D2__NACC__EE_SD

tag: rat

value: KH L07 D2

value: social defeat stress (SD)

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: bLR_RatL11_A2_NACC__EE_SD

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: distance traveled (open field habituation)

value: Good


title: CD138hi, bone marrow, P0544, BCR

description: 5' BCR seq

tag: tissue

tag: cell type

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

tag: library type

value: mRNA


title: AGI881_P1_H05_S89, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: CD138hi, bone marrow, P0544, GEX

description: 5' polyA RNA


title: CD138hi, bone marrow, P0274-P0487V2, ADT-HTO

source_name: Bone marrow / Peripheral blood

value: Bone marrow / Peripheral blood

value: ADT/HTO

tag: adt

value: C0050_anti-human-CD19, C0831_anti-human-CD138, C0410_anti-human-CD38, WT-Spike_Oligo-1, Omicron-Spike_Oligo-2, TotalSeq-C0100 anti-human CD20, C_0154-anti-human-CD27, C0136_anti-human-IgM-Antibody, C0384_anti-human-IgD-Antibody

tag: hto

value: C0251_anti-human-Hashtag-1, C0252_anti-human-Hashtag-2, C0253_anti-human-Hashtag-3, C0254_anti-human-Hashtag-4, C0255 anti-human Hashtag 5


title: CD138hi, bone marrow, P0520, BCR

description: 5' BCR seq

value: Bone marrow

value: Plasma cell


title: bLR_RatL11_A1_NACC__EE_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: AGI881_P1_G10_S82, Smart-seq2 (multi-omics)

tag: tissue

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)

value: Yes


title: AGI881_P1_H02_S86, Smart-seq2 (multi-omics)


title: bLR_RatKH_L07_C2_NACC__EE_SD

tag: rat

value: KH L07 C2

tag: hemisphere

value: left

value: bred Low Responder (bLR)

tag: family

tag: date of sacrifice

tag: date of dissection

tag: distance traveled (open field habituation)


title: CD138hi, bone marrow, P0520, GEX

description: 5' polyA RNA

tag: cell type

tag: participant 1_id

tag: participant 1_sex

value: Female

tag: participant 1_food_allergy_status

value: Allergic

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

tag: library type


title: CD138hi, bone marrow, P0274-P0487V2, GEX

description: 5' polyA RNA

value: Male

value: Non-allergic


title: CD138hi, bone marrow, P0435, BCR

description: 5' BCR seq


title: AGI881_P1_H01_S85, Smart-seq2 (multi-omics)


title: CD138hi, bone marrow, P0435, GEX

description: 5' polyA RNA


title: AGI881_P1_G12_S84, Smart-seq2 (multi-omics)


title: CD138hi, bone marrow, P0450-P0487V1, ADT-HTO

tag: hto

value: C0251_anti-human-Hashtag-1, C0252_anti-human-Hashtag-2, C0253_anti-human-Hashtag-3, C0254_anti-human-Hashtag-4


title: CD138hi, bone marrow, P0544, ADT-HTO

tag: tissue

tag: adt


title: AGI881_P1_G08_S80, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: AGI881_P1_G11_S83, Smart-seq2 (multi-omics)


title: CD138hi, bone marrow, P0274-P0487V2, BCR

description: 5' BCR seq

value: mRNA


title: CD138hi, bone marrow, P0520, ADT-HTO


title: HBMECs, 20mM, biological replicate 3

city: Beijing

first: Qiheng

last: He

state: Beijing

address: 119 South Fourth Ring West Road, Fengtai District

department: Neurosurgery

institute: Beijing Tiantan Hospital

data_processing:
The image data measured by the high-throughput sequencer are converted intosequence data (reads)by CASAVA base recognition. Raw data (raw reads) of fastgformat were firstly processed through in-house perl scripts.In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing Nbase and low quality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2(v2.0.5)and paired-end clean reads were aligned to the reference genome usingHisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate adatabase of splice junctions based on the gene model annotation file and thus a bettermapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene. FPKM, expected number of Fragments PerKilobase of transcript sequence per Millions base pairs sequenced, considers theeffect of sequencing depth and gene length for the reads count at the same time, and iscurrently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: HBMEC

growth_protocol: HBMECs (#1000, ScienCell, USA) were cultured in endothelial cell medium (ECM, #1001, ScienCell, USA) with 5% FBS according to the manufacturer’s guidelines and were not used beyond passage 10. The HBMECs were cultured and maintained in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol:
TRIzol (#15596-018, Ambion, USA) was used to obtain total RNA from the samples for RNA-seq.
Total RNA was used as input material for the RNA sample preparations. BrieflymRNA was purified from total RNA by using poly-T oligo-attached magnetic beadsFragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized usingrandom hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH todegrade the RNA. Second strand cDNA synthesis was subsequently performed usingDNA Polymerase I and dNTP. Remaining overhangs were converted into blunt endsvia exonuclease/polymerase activities. After adenylation of 3’ends of DNAfragments, Adaptor with hairpin loop structure were ligated to prepare forhybridization.In order to select cDNA fragments of preferentially 370~420 bp inlength, the library fiagments were purified with AMPure XP system (BeckmanCoulter, Beverly, USA). Then PCR amplification, the PCR product was purified byAMPure XP beads, and the library was finally obtained.

tag: cell line

value: HBMEC

value: endothelial cells

tag: treatment

value: 20mM glutamine


title: bLR_RatKH_L07_C1_NACC__EE_SD

tag: rat

value: KH L07 C1

tag: hemisphere

tag: animal strain

tag: social defeat stress

value: social defeat stress (SD)

tag: adolescent environmental enrichment

value: social and environmental enrichment (EE)

tag: generation

tag: family

tag: date of sacrifice

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: CD138hi, bone marrow, P0450-P0487V1, BCR

description: 5' BCR seq

tag: tissue

value: Bone marrow

tag: cell type

value: Plasma cell

tag: participant 1_id

tag: participant 1_sex

tag: participant 1_food_allergy_status

tag: participant 2_id

tag: participant 2_sex

tag: participant 2_food_allergy_status

tag: library type


title: AGI881_P1_G09_S81, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)

value: Yes


title: bLR_RatKH_L07_B2_NACC__EE_NIL

tag: rat

value: KH L07 B2

tag: hemisphere

value: left

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

value: no social defeat stress (NIL)

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: distance traveled (open field habituation)

value: Good


title: bLR_RatKH_L07_A1_NACC__EE_NIL

value: KH L07 A1

value: right

tag: plasma testosterone (pg/ml)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: HBMECs, 20mM, biological replicate 2

tag: cell line

value: HBMEC

tag: cell type

tag: treatment


title: bLR_RatKH_L07_A2_NACC__EE_NIL

tag: rat

value: KH L07 A2

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family


title: bLR_RatL11_B3_NACC__EE_NIL

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: distance traveled (open field habituation)


title: AGI881_P1_G04_S76, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: HBMECs, 0mM, biological replicate 2

tag: cell line

tag: cell type

value: endothelial cells

tag: treatment

value: no glutamine


title: AGI881_P1_G05_S77, Smart-seq2 (multi-omics)


title: CD138hi, bone marrow, P0450-P0487V1, GEX

description: 5' polyA RNA

tag: participant 1_id

tag: participant 1_sex

value: Male

tag: participant 1_food_allergy_status

value: Non-allergic

tag: participant 2_id

tag: participant 2_sex

value: Female

tag: participant 2_food_allergy_status

value: Allergic

tag: library type

value: mRNA


title: HBMECs, 0mM, biological replicate 1


title: HBMECs, 0mM, biological replicate 3


title: AGI881_P1_G02_S74, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell

value: Yes


title: Alveolar organoids, tissue

first: Carla

last: Kim

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
cellranger v7.1
Assembly: human_GRC38
Supplementary files format and content: matrix files

source_name: Lung

extract_protocol:
Organoids were prepared for scRNA-seq by incubation in TrypLE at 37°C, gently pipetting once every 5-10 min, up to 40 min, to achieve a single-cell suspension. Cells were passed through a 40-µm mesh filter. Viable cells were selected using a Dead Cell Removal kit (Miltenyi Biotec) and resuspended in PBS with 10% FBS and 10 µM Y-27632, at a concentration of 1,000 cells/µl.
Single-cell libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3’ v3.1 kits

value: Lung

value: Epithelial


title: Alveolar organoids, BAL, biol rep 2

description: 10X Genomics


title: bLR_RatL11_B2_NACC__EE_NIL

tag: rat

tag: hemisphere

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

value: no social defeat stress (NIL)

tag: adolescent environmental enrichment

value: social and environmental enrichment (EE)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: plasma testosterone (pg/ml)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: AGI881_P1_G01_S73, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: Alveolar organoids, BAL, biol rep 1

description: 10X Genomics

tag: cell type


title: bLR_RatKH_L07_B1_NACC__EE_NIL

tag: rat

value: KH L07 B1

tag: hemisphere

value: right

tag: animal strain

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: distance traveled (open field habituation)

value: Good


title: Airway organoids, tissue

description: 10X Genomics


title: bLR_RatL11_B1_NACC__EE_NIL

value: left

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction


title: Airway organoids, BAL, biol rep 2

description: 10X Genomics

tag: tissue


title: AGI881_P1_F11_S71, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: Airway organoids, BAL, biol rep 1

description: 10X Genomics

tag: cell type


title: bLR_RatL08_D2_NACC__NIL_SD

tag: rat

value: social defeat stress (SD)

value: standard housing (NIL)

tag: plasma testosterone (pg/ml)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: HBMECs, 20mM, biological replicate 1

tag: cell line

value: HBMEC

value: endothelial cells

tag: treatment

value: 20mM glutamine


title: bLR_RatL08_D1_NACC__NIL_SD

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: distance traveled (open field habituation)


title: A253 cells, sgRNA SOX2, rep2

city: Madrid

first: Ana

last: Sastre-Perona

state: Madrid

address: Calle Paseo de la Castellana 261, INGEMM, Laboratorio de Epigenética, Hospital Universitario La Paz

country: Spain

institute: IdiPAZ

data_processing:
Mapping was done using HISAT2
StringTie was used for transcriptome assembly
Deseq was used to identify differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-delimited tex file includes raw counts for each sample

source_name: Salivary gland

growth_protocol: A253 control or know-out cells were grown in DMEM supplemented with 10% FBS and humidified atmosphenre at 5% CO2 at 37C

extract_protocol:
total RNA was extracted using Trizol and the microprep RNA extraction kit, Zymo
RNA libraries for RNA-seq were prepared using  the llumina® Stranded mRNA Prep and following the manufacture's instructions

tag: tissue

value: Salivary gland

tag: cell type

value: Salivary gland SCC

tag: genotype

value: SOX2 KO